Welcome. It depends on what you want to do with the results. If you want to update one folder from the other (that is: see if files on one are present on the other and if not copy them over) then rsync does the job perfectly. But if all you want to do is seeing if there's a difference between the folders, the diff tool has to be your choice. It compares 2 text files, and those text files can be generated by having the output of the ls command piped to a text file. Mind, it's commandline stuff, so get your DOS hat on and be prepared for a shock: bash (the standard Linux shell) is much more powerful then you'd ever imagined

Yes I have a mountain of stuff to learn regarding the Linux OS let alone the web application that we are going to be running our website on.

That is a great idea doing a dump of the outputs to a text file and then comparing them. I know there is then going to be files that I will need to get over to the Ubuntu server. Is there any tools that you would then recommend for then connecting to the machine to be able to copy the files over?

[url="http://www.cis.upenn.edu/~bcpierce/unison/"]Unison[/url] sounds like a perfect fit for this job.

Unison is a file-synchronization tool for Unix and Windows. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other.

I haven't tried the Windows version but use it many times each day for synchronising Linux boxes.

"Insanity: doing the same thing over and over again and expecting different results." (Albert Einstein)

I recommend Unison, too, I use it on both Linux and Windows. When installing on Windows, you will also need to install something called GTK+ for Windows Runtime Environment, it's a tool-kit for drawing Unison's GUI. After installing it, you may then need to add its location to your "Path" environment variable (if the installer didn't already do so) which should be here:

With two collections stored on media that use different file systems (as is the case with Linux and Windows), Unison may throw up an error when it tries to synchronise the permissions of the files. If this happens, add the following lines to Unison's profile files (located at ~/.unison/*.prf on Linux and C:\Documents and Settings\<user>\.unison\*.prf on Windows):

Install on both. It has to be the same version, but that's unlikely to be a problem. It uses SSH to communicate, so you just need to set up key authentication for the user(s) - but you should have that anyway.

"Insanity: doing the same thing over and over again and expecting different results." (Albert Einstein)